Question: Low mapping of paired-end reads with tophat2
gravatar for Aragion
23 months ago by
Aragion0 wrote:

Hello. I'm trying to map paired-end reads on reference scaffold using tophat2. But the percentage if mapped reads is almost 0%

Left reads: Input: 9526882

Mapped: 224 ( 0.0% of input)

of these: 22 ( 9.8%) have multiple alignments (0 have >20)

Right reads: Input: 9526882

Mapped: 230 ( 0.0% of input)

of these: 18 ( 7.8%) have multiple alignments (0 have >20)

0.0% overall read mapping rate.

Aligned pairs: 111 of these: 5 ( 4.5%) have multiple alignments

0.0% concordant pair alignment rate.

I've tried to change tophat2 options (like intron length and inner distance) and to map unmapped reads, but the result is always the same. Any suggestions are appreciated. Thanks.

tophat • 1.1k views
ADD COMMENTlink modified 23 months ago by Jennifer Hillman Jackson25k • written 23 months ago by Aragion0
gravatar for Jennifer Hillman Jackson
23 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The most common reason I have seen that causes this problem is incorrect quality score scaling (and datatype assignment) of the input fastq datasets. How to check:

Other reasons can include: mismatched paired-end files, incorrect target genome selection, and poor quality of the reads (trimming artifact may help). FastQC can be used to access quality.

If you do end up running the Fastq Groomer tool to adjust quality scores to fastqsanger, run it again on the updated fastq dataset. Don't use the report based on the original fastq dataset unless it reports the sequences are already in fastqsanger format, as explained in the help link above.

Best, Jen, Galaxy team

ADD COMMENTlink modified 22 months ago • written 23 months ago by Jennifer Hillman Jackson25k
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